Biomedical subjects

Jen-Shiang K Yu

Publications and source records attributed to Jen-Shiang K Yu.

3 recordsLinked to original sources

PubMed2006

A three-coordinate and quadruply bonded Mo-Mo complex.

Reaction of MoCl3(THF)3 with [Me2Si{NLi(Dipp)}2]2 (Dipp = 2,6-i-PrC6H3) afforded a triply bonded dimolybdenum complex 1,2-Mo2Cl2[Me2Si(NDipp)2]2 1, spanned by two Me2Si[N(Dipp)]2 ligands, thus resulting in a syn conformation. The air- and moisture-sensitive compound 1 was characterized by NMR spectroscopic, elemental, and single-crystal X-ray crystallographic analysis. Reduction of 1 by Na/Hg yielded the quadruply bonded dimeric complex Mo2[Me2Si(NDipp)2]2 2, which was also characterized by the aforementioned analytical methods. The Mo-Mo bond was determined to be 2.1784(12) A, which is considered a long quadruple bond. In addition, density functional theory (DFT) computations on compound 2 provided insight into the intriguing Mo-Mo quadruple bond.

Crystallography↗

PubMedDate not supplied

Recent advances in PC-Linux systems for electronic structure computations by optimized compilers and numerical libraries.

One of the most frequently used packages for electronic structure research, GAUSSIAN 98, is compiled on Linux systems with various hardware configurations, including AMD Athlon (with the "Thunderbird" core), AthlonMP, and AthlonXP (with the "Palomino" core) systems as well as the Intel Pentium 4 (with the "Willamette" core) machines. The default PGI FORTRAN compiler (pgf77) and the Intel FORTRAN compiler (ifc) are respectively employed with different architectural optimization options to compile GAUSSIAN 98 and test the performance improvement. In addition to the BLAS library included in revision A.11 of this package, the Automatically Tuned Linear Algebra Software (ATLAS) library is linked against the binary executables to improve the performance. Various Hartree-Fock, density-functional theories, and the MP2 calculations are done for benchmarking purposes. It is found that the combination of ifc with ATLAS library gives the best performance for GAUSSIAN 98 on all of these PC-Linux computers, including AMD and Intel CPUs. Even on AMD systems, the Intel FORTRAN compiler invariably produces binaries with better performance than pgf77. The enhancement provided by the ATLAS library is more significant for post-Hartree-Fock calculations. The performance on one single CPU is potentially as good as that on an Alpha 21264A workstation or an SGI supercomputer. The floating-point marks by SpecFP2000 have similar trends to the results of GAUSSIAN 98 package.

Journal Article↗

PubMedDate not supplied

Numerical performance and throughput benchmark for electronic structure calculations in PC-Linux systems with new architectures, updated compilers, and libraries.

A number of recently released numerical libraries including Automatically Tuned Linear Algebra Subroutines (ATLAS) library, Intel Math Kernel Library (MKL), GOTO numerical library, and AMD Core Math Library (ACML) for AMD Opteron processors, are linked against the executables of the Gaussian 98 electronic structure calculation package, which is compiled by updated versions of Fortran compilers such as Intel Fortran compiler (ifc/efc) 7.1 and PGI Fortran compiler (pgf77/pgf90) 5.0. The ifc 7.1 delivers about 3% of improvement on 32-bit machines compared to the former version 6.0. Performance improved from pgf77 3.3 to 5.0 is also around 3% when utilizing the original unmodified optimization options of the compiler enclosed in the software. Nevertheless, if extensive compiler tuning options are used, the speed can be further accelerated to about 25%. The performances of these fully optimized numerical libraries are similar. The double-precision floating-point (FP) instruction sets (SSE2) are also functional on AMD Opteron processors operated in 32-bit compilation, and Intel Fortran compiler has performed better optimization. Hardware-level tuning is able to improve memory bandwidth by adjusting the DRAM timing, and the efficiency in the CL2 mode is further accelerated by 2.6% compared to that of the CL2.5 mode. The FP throughput is measured by simultaneous execution of two identical copies of each of the test jobs. Resultant performance impact suggests that IA64 and AMD64 architectures are able to fulfill significantly higher throughput than the IA32, which is consistent with the SpecFPrate2000 benchmarks.

Journal Article↗